..

.gitignore

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+ompiled source #
+###################
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.so
+
+# Packages #
+############
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.dmg
+*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.zip
+
+# Logs and databases #
+######################
+*.sql
+*.sqlite
+*.mat
+*.edges
+*.smat
+*.labels
+*.graphml
+*.gephi
+*.png
+*.eps
+*.jpg
+
+# OS generated files #
+######################
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+Icon?
+ehthumbs.db
+Thumbs.db
+.settings/
+.cproject
+.project
+.pydevproject
+data/
+exp/
+
+
+#Latex #
+##############
+*.acn
+*.acr
+*.alg
+*.aux
+*.bbl
+*.blg
+*.dvi
+*.fdb_latexmk
+*.glg
+*.glo
+*.gls
+*.idx
+*.ilg
+*.ind
+*.ist
+*.lof
+*.log
+*.lot
+*.maf
+*.mtc
+*.mtc0
+*.nav
+*.nlo
+*.out
+*.pdfsync
+*.ps
+*.snm
+*.synctex.gz
+*.toc
+*.vrb
+*.xdy

LICENSE.md

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+License
+-------
+**Parallel Maximum Clique (PMC) Library**,
+Copyright (C) 2012-2013: Ryan A. Rossi, All rights reserved.
+
+>This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+>This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+>You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+If used, please cite the following manuscript:
+
+	Ryan A. Rossi, David F. Gleich, Assefaw H. Gebremedhin, Md. Mostofa
+	Patwary, A Fast Parallel Maximum Clique Algorithm for Large Sparse Graphs
+	and Temporal Strong Components, arXiv 2013

Makefile

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+#
+# Makefile for PMC
+#
+# Ryan A. Rossi
+# Copyright, 2012-2013
+#
+
+.KEEP_STATE:
+
+all: pmc
+
+OPTFLAGS    = -O3
+CFLAGS      = $(OPTFLAGS)
+CXX          = g++
+H_FILES     = pmc.h
+
+.cpp.o:
+	$(CXX) $(CFLAGS) -c $<
+
+IO_SRC 				   = pmc_utils.cpp \
+						pmc_graph.cpp \
+						pmc_clique_utils.cpp
+
+PMC_SRC 			   = pmc_heu.cpp \
+						pmc_maxclique.cpp \
+						pmcx_maxclique.cpp \
+						pmcx_maxclique_basic.cpp
+
+BOUND_LIB_SRC 		   = pmc_cores.cpp 
+
+PMC_MAIN			   = pmc_driver.cpp
+
+OBJ_PMC	= $(PMC_MAIN:%.cpp=%.o) $(IO_SRC) $(PMC_SRC) $(BOUND_LIB_SRC)
+$(OBJ_PMC): $(H_FILES) Makefile
+pmc: $(OBJ_PMC) $(H_FILES)
+	$(CXX) $(CFLAGS) -o pmc $(OBJ_PMC) -fopenmp
+
+clean:
+	rm -rf *.o pmc

README.md

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+Parallel Maximum Clique (PMC) Library
+=====================================
+
+In short, a parameterized high performance library for computing maximum cliques in large sparse graphs.
+
+Finding maximum cliques, k-cliques, and temporal strong components are in general NP-hard.
+Yet, these can be computed fast in most social and information networks.
+The PMC library is designed to be fast for solving these problems.
+Algorithms in the PMC library are easily adaptable for use with a variety of orderings, heuristic strategies, and bounds.
+
+* **Maximum clique:** 		 Given a simple undirected graph G and a number k, output the clique of largest size.
+* **K-clique:** 	   		 In k-clique, the problem is to find a clique of size k if one exists.
+* **Largest temporal-scc:** Given a temporal graph G, a temporal strong component is a set of vertices where all temporal paths exist between the vertices in that set. The Largest TSCC problem is to find the largest among all the temporal strong components.
+
+
+
+Features
+--------
+0.  General framework for parallel maximum clique algorithms
+1.	Optimized to be fast for large sparse graphs 
+	+ 	Algorithms tested on networks of 1.8 billion edges
+2.	Set of fast heuristics shown to give accurate approximations
+3.	Algorithms for computing Temporal Strongly Connected Components (TSCC) of large dynamic networks
+4.	Parameterized for computing k-cliques as fast as possible
+5.  Includes a variety of tight linear time bounds for the maximum clique problem
+6.  Ordering of vertices for each algorithm can be selected at runtime 
+7.  Dynamically reduces the graph representation periodically as vertices are pruned or searched
+	+   Lowers memory-requirements for massive graphs, increases speed, and has caching benefits
+
+
+Synopsis
+---------
+
+### Setup
+First, you'll need to compile the parallel maximum clique library.  
+
+		$ cd path/to/pmc/
+		$ make
+
+Afterwards, the following should work:  
+
+		# compute maximum clique using the full algorithm `-a 0`
+		./pmc -f data/socfb-Texas84.mtx -a 0
+
+
+*PMC* has been tested on Ubuntu linux (10.10 tested) and Mac OSX (Lion tested) with gcc-mp-4.7 and gcc-mp-4.5.4
+
+Please let me know if you run into any issues.  
+
+
+
+### Input file format
++ Matrix Market Coordinate Format (symmetric)  
+For details see: <http://math.nist.gov/MatrixMarket/formats.html#MMformat>  
+
+		%%MatrixMarket matrix coordinate pattern symmetric  
+		4 4 6  
+		2 1  
+		3 1  
+		3 2  
+		4 1  
+		4 2  
+		4 3 
+
+
++ Edge list (symmetric and unweighted):
+		Codes for transforming the graph into the correct format are provided in the experiments directory.
+
+
+Overview
+---------
+
+The parallel maximum clique algorithms use tight bounds that are fast to compute.
+A few of those are listed below.
+
+* K-cores
+* Degree
+* Neighborhood cores
+* Greedy coloring
+
+All bounds are dynamically updated.  
+
+Examples of the three main maximum clique algorithms are given below.
+Each essentially builds on the other.
+
+	# uses the four basic k-core pruning steps
+	./pmc -f ../pmc/data/output/socfb-Stanford3.mtx -a 2
+
+	# k-core pruning and greedy coloring
+	./pmc -f ../pmc/data/output/socfb-Stanford3.mtx -a 1
+
+	# neighborhood core pruning (and ordering for greedy coloring)
+	./pmc -f ../pmc/data/output/socfb-Stanford3.mtx -a 0
+
+
+
+
+
+### Dynamic graph reduction
+
+The reduction wait parameter `-r` below is set to be 1 second (default = 4 seconds).
+
+	./pmc -f data/sanr200-0-9.mtx -a 0 -t 2 -r 1
+
+In some cases, it may make sense to turn off the explicit graph reduction. 
+This is done by setting the reduction wait time '-r' to be very large.
+
+	# Set the reduction wait parameter
+	./pmc -f data/socfb-Stanford3.mtx -a 0 -t 2 -r 999
+
+
+
+
+
+
+### Orderings
+
+The PMC algorithms are easily adapted to use various ordering strategies. 
+To prescribe a vertex ordering, use the -o option with one of the following:
++ `deg`
++ `kcore`
++ `dual_deg`&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;orders vertices by the sum of degrees from neighbors
++ `dual_kcore`&nbsp;&nbsp;orders vertices by the sum of core numbers from neighbors
++ `kcore_deg`&nbsp;&nbsp;&nbsp; vertices are ordered by the weight k(v)d(v)
++ `rand`&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; randomized ordering of vertices
+
+
+
+##### Direction of ordering
+
+Vertices are searched by default in increasing order, to search vertices in decreasing order, use the `d` option:
+
+	./pmc -f data/p-hat700-2.mtx -a 0 -d
+
+
+
+
+### Heuristic
+The fast heuristic may also be customized to use various greedy selection strategies.
+This is done by using `-h` with one of the following: 
+
++ `deg`
++ `kcore`
++ `kcore_deg`&nbsp;&nbsp;&nbsp; select vertex that maximizes k(v)d(v)
++ `rand`&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; randomly select vertices
+
+
+#### Terminate after applying the heuristic
+Approximate the maximum clique using _ONLY_ the heuristic by not setting the exact algorithm via the `-a [num]` option.
+For example:  
+
+	./pmc -f data/sanr200-0-9.mtx -h deg
+
+#### Turning the heuristic off
+
+	# heuristic is turned off by setting `-h 0`.
+	./pmc -f data/tscc_enron-only.mtx -h 0 -a 0
+
+
+
+### K-clique
+
+The parallel maximum clique algorithms have also been parameterized to find cliques of size k.
+This routine is useful for many tasks in network analysis such as mining graphs and community detection.
+
+	# Computes a clique of size 50 from the Stanford facebook network
+	./pmc -f data/socfb-Stanford3.mtx -a 0 -k 50
+
+
+using `-o rand` to find potentially different cliques of a certain size
+
+	# Computes a clique of size 36 from sanr200-0-9
+	./pmc -f data/sanr200-0-9.mtx -a 0 -k 36 -o rand
+
+
+
+Terms and conditions
+--------------------
+Please feel free to use these codes. We only ask that you cite:  
+
+	Ryan A. Rossi, David F. Gleich, Assefaw H. Gebremedhin, Md. Mostofa Patwary,  
+	A Fast Parallel Maximum Clique Algorithm for Large Sparse Graphs and Temporal  
+	Strong Components, arXiv preprint 1302.6256, 2013.  
+
+_These codes are research prototypes and may not work for you. No promises. But do email if you run into problems._
+
+
+Copyright 2011-2013, Ryan A. Rossi. All rights reserved.
+

pmc.h

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+/**
+ ============================================================================
+ Name        : Parallel Maximum Clique (PMC) Library
+ Author      : Ryan A. Rossi   (rrossi@purdue.edu)
+ Description : A general high-performance parallel framework for computing
+               maximum cliques. The library is designed to be fast for large
+               sparse graphs.
+
+ Copyright (C) 2012-2013, Ryan A. Rossi, All rights reserved.
+
+ Please cite the following paper if used:
+   Ryan A. Rossi, David F. Gleich, Assefaw H. Gebremedhin, Md. Mostofa
+   Patwary, A Fast Parallel Maximum Clique Algorithm for Large Sparse Graphs
+   and Temporal Strong Components, arXiv preprint 1302.6256, 2013.
+
+ See http://ryanrossi.com/pmc for more information.
+ ============================================================================
+ */
+
+#ifndef __PMC_H__
+#define __PMC_H__
+
+#include "pmc_headers.h"
+#include "pmc_input.h"
+#include "pmc_utils.h"
+
+#include "pmc_heu.h"
+#include "pmc_maxclique.h"
+#include "pmcx_maxclique.h"
+#include "pmcx_maxclique_basic.h"
+
+#endif